/EXTERNAL BLUEPRINT/variants/K006326_15_lane_gembs
BACK
SAMPLE K006326_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1096001565 |
597362491 |
54.50 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1096001565 |
100% |
1076549728 |
98.23 % |
19451837 |
1.77 % |
| |
|
|
|
|
|
|
| Passed |
599004694 |
54.65 % |
596167490 |
55.38 % |
2837204 |
0.47 % |
| Filtered |
496996871 |
45.35 % |
480382238 |
44.62 % |
16614633 |
2.77 % |
| |
|
|
|
|
|
|
| q20 |
406778363 |
81.85 % |
404922733 |
84.29 % |
1855630 |
11.17 % |
| q20,qd2 |
59450141 |
11.96 % |
45276744 |
9.43 % |
14173397 |
85.31 % |
| q20,mq40 |
14853973 |
2.99 % |
14748933 |
3.07 % |
105040 |
0.63 % |
| mq40 |
7404694 |
1.49 % |
7244954 |
1.51 % |
159740 |
0.96 % |
| qd2 |
4992148 |
1.00 % |
4894644 |
1.02 % |
97504 |
0.59 % |
| q20,qd2,mq40 |
3404249 |
0.68 % |
3206309 |
0.67 % |
197940 |
1.19 % |
| qd2,mq40 |
101225 |
0.02 % |
87921 |
0.02 % |
13304 |
0.08 % |
| q20,qd2,fs60 |
4298 |
0.00 % |
0 |
0.00 % |
4298 |
0.03 % |
| fs60 |
2409 |
0.00 % |
0 |
0.00 % |
2409 |
0.01 % |
| qd2,fs60 |
2262 |
0.00 % |
0 |
0.00 % |
2262 |
0.01 % |
| qd2,fs60,mq40 |
1703 |
0.00 % |
0 |
0.00 % |
1703 |
0.01 % |
| q20,qd2,fs60,mq40 |
757 |
0.00 % |
0 |
0.00 % |
757 |
0.00 % |
| fs60,mq40 |
642 |
0.00 % |
0 |
0.00 % |
642 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
3170330 |
10.67 % |
| Transition |
G>A |
All |
10497260 |
35.33 % |
| Transition |
T>C |
All |
2906547 |
9.78 % |
| Transition |
C>T |
All |
10309289 |
34.70 % |
| Transversion |
A>C |
All |
216125 |
0.73 % |
| Transversion |
C>A |
All |
574329 |
1.93 % |
| Transversion |
T>G |
All |
236428 |
0.80 % |
| Transversion |
G>T |
All |
562811 |
1.89 % |
| Transversion |
A>T |
All |
429136 |
1.44 % |
| Transversion |
T>A |
All |
431633 |
1.45 % |
| Transversion |
C>G |
All |
194746 |
0.66 % |
| Transversion |
G>C |
All |
184276 |
0.62 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
344042 |
19.30 % |
| Transition |
G>A |
Passed |
305178 |
17.12 % |
| Transition |
T>C |
Passed |
341652 |
19.17 % |
| Transition |
C>T |
Passed |
305133 |
17.12 % |
| Transversion |
A>C |
Passed |
65282 |
3.66 % |
| Transversion |
C>A |
Passed |
58606 |
3.29 % |
| Transversion |
T>G |
Passed |
64976 |
3.65 % |
| Transversion |
G>T |
Passed |
58728 |
3.29 % |
| Transversion |
A>T |
Passed |
39010 |
2.19 % |
| Transversion |
T>A |
Passed |
39108 |
2.19 % |
| Transversion |
C>G |
Passed |
80295 |
4.50 % |
| Transversion |
G>C |
Passed |
80512 |
4.52 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
9.50 |
26883426 |
2829484 |
| Passed |
2.66 |
1296005 |
486517 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |